He was the face of "bad" Microsoft, the unashamedly anti-competitive win-at-all-costs bully. Gates could win some people back with his nerd-cred and things like the mid-'00s "security push". Ballmer was first and foremost a suit, or rather a suit trying to pretend he's down with the nerds just enough to screw them as soon as they turn around, and his "fuck you" attitude wasn't exactly friendly.
> I'm don't think Ballmer's list of accomplishments at Microsoft is fully appreciated
Probably because they were accomplishments for Microsoft rather than for the industry as a whole. Apple gets a lot of leeway because the iPhone really made a difference for the industry, not just winning but drawing a path. Microsoft has not really done anything like that since the Win 95 / Office / IE 5 progression.